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[Feature] Package Export/Import (#116)

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Fixes #90
Fixes #91
Fixes #115
Fixes #104

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#116
This commit is contained in:
jebus
2025-09-16 02:41:10 +12:00
parent ce349a287b
commit 762a6b7baf
32 changed files with 2500683 additions and 145 deletions
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65
epdb/management/commands/bootstrap.py
View File

@ -12,21 +12,24 @@ class Command(BaseCommand):
def create_users(self):
if not User.objects.filter(email='anon@lorsba.ch').exists():
anon = UserManager.create_user("anonymous", "anon@lorsba.ch", "SuperSafe", is_active=True,
add_to_group=False, set_setting=False)
# Anonymous User
if not User.objects.filter(email='anon@envipath.com').exists():
anon = UserManager.create_user("anonymous", "anon@envipath.com", "SuperSafe",
is_active=True, add_to_group=False, set_setting=False)
else:
anon = User.objects.get(email='anon@lorsba.ch')
anon = User.objects.get(email='anon@envipath.com')
if not User.objects.filter(email='admin@lorsba.ch').exists():
admin = UserManager.create_user("admin", "admin@lorsba.ch", "SuperSafe", is_active=True, add_to_group=False,
set_setting=False)
# Admin User
if not User.objects.filter(email='admin@envipath.com').exists():
admin = UserManager.create_user("admin", "admin@envipath.com", "SuperSafe",
is_active=True, add_to_group=False, set_setting=False)
admin.is_staff = True
admin.is_superuser = True
admin.save()
else:
admin = User.objects.get(email='admin@lorsba.ch')
admin = User.objects.get(email='admin@envipath.com')
# System Group
g = GroupManager.create_group(admin, 'enviPath Users', 'All enviPath Users')
g.public = True
g.save()
@ -40,25 +43,25 @@ class Command(BaseCommand):
admin.default_group = g
admin.save()
if not User.objects.filter(email='jebus@lorsba.ch').exists():
jebus = UserManager.create_user("jebus", "jebus@lorsba.ch", "SuperSafe", is_active=True, add_to_group=False,
set_setting=False)
jebus.is_staff = True
jebus.is_superuser = True
jebus.save()
if not User.objects.filter(email='user0@envipath.com').exists():
user0 = UserManager.create_user("user0", "user0@envipath.com", "SuperSafe",
is_active=True, add_to_group=False, set_setting=False)
user0.is_staff = True
user0.is_superuser = True
user0.save()
else:
jebus = User.objects.get(email='jebus@lorsba.ch')
user0 = User.objects.get(email='user0@envipath.com')
g.user_member.add(jebus)
g.user_member.add(user0)
g.save()
jebus.default_group = g
jebus.save()
user0.default_group = g
user0.save()
return anon, admin, g, jebus
return anon, admin, g, user0
def import_package(self, data, owner):
return PackageManager.import_package(data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True)
return PackageManager.import_legacy_package(data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True)
def create_default_setting(self, owner, packages):
s = SettingManager.create_setting(
@ -108,13 +111,6 @@ class Command(BaseCommand):
'base_url': 'https://www.rhea-db.org',
'url_pattern': 'https://www.rhea-db.org/rhea/{id}'
},
{
'name': 'CAS',
'full_name': 'Chemical Abstracts Service Registry',
'description': 'Registry of chemical substances',
'base_url': 'https://www.cas.org',
'url_pattern': None # CAS doesn't have a free public URL pattern
},
{
'name': 'KEGG Reaction',
'full_name': 'KEGG Reaction Database',
@ -122,13 +118,6 @@ class Command(BaseCommand):
'base_url': 'https://www.genome.jp',
'url_pattern': 'https://www.genome.jp/entry/reaction+{id}'
},
{
'name': 'MetaCyc',
'full_name': 'MetaCyc Metabolic Pathway Database',
'description': 'Database of metabolic pathways and enzymes',
'base_url': 'https://metacyc.org',
'url_pattern': None
},
{
'name': 'UniProt',
'full_name': 'MetaCyc Metabolic Pathway Database',
@ -147,7 +136,9 @@ class Command(BaseCommand):
@transaction.atomic
def handle(self, *args, **options):
# Create users
anon, admin, g, jebus = self.create_users()
anon, admin, g, user0 = self.create_users()
self.populate_common_external_databases()
# Import Packages
packages = [
@ -169,7 +160,7 @@ class Command(BaseCommand):
setting.save()
setting.make_global_default()
for u in [anon, jebus]:
for u in [anon, user0]:
u.default_setting = setting
u.save()
@ -200,6 +191,6 @@ class Command(BaseCommand):
ml_model.build_model()
# ml_model.evaluate_model()
# If available create EnviFormerModel
# If available, create EnviFormerModel
if s.ENVIFORMER_PRESENT:
enviFormer_model = EnviFormer.create(pack, 'EnviFormer - T0.5', 'EnviFormer Model with Threshold 0.5', 0.5)

2
epdb/management/commands/import_package.py → epdb/management/commands/import_legacy_package.py
View File

@ -24,4 +24,4 @@ class Command(BaseCommand):
def handle(self, *args, **options):
owner = User.objects.get(username=options['owner'])
package_data = json.load(open(options['data']))
PackageManager.import_package(package_data, owner)
PackageManager.import_legacy_package(package_data, owner)